chr1-151760903-CAAAAAAAAAAA-C

Variant names:

• chr1-151760903-CAAAAAAAAAAA-C
• rs755031728
• NM_031420.4:c.589-15_589-5delTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_031420.4(MRPL9):​c.589-15_589-5delTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000455 in 879,710 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000045 (0 hom.)
• Consequence: MRPL9 NM_031420.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16
• Publications: 0 publications found

Genes affected

MRPL9 (HGNC:14277): (mitochondrial ribosomal protein L9) This is a nuclear gene encoding a protein component of the 39S subunit of the mitochondrial ribosome. Alternative splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 8. [provided by RefSeq, Jul 2014]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031420.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPL9	NM_031420.4	MANE Select	c.589-15_589-5delTTTTTTTTTTT		splice_region intron	N/A	NP_113608.1	Q9BYD2
	MRPL9	NM_001300733.2		c.487-15_487-5delTTTTTTTTTTT		splice_region intron	N/A	NP_001287662.1	Q5SZR1
	MRPL9	NR_125331.2		n.646-15_646-5delTTTTTTTTTTT		splice_region intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPL9	ENST00000368830.8	TSL:1 MANE Select	c.589-15_589-5delTTTTTTTTTTT		splice_region intron	N/A	ENSP00000357823.3	Q9BYD2
	MRPL9	ENST00000368829.3	TSL:2	c.487-15_487-5delTTTTTTTTTTT		splice_region intron	N/A	ENSP00000357822.3	Q5SZR1
	MRPL9	ENST00000495867.1	TSL:2	n.7_17delTTTTTTTTTTT		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000455 AC: 4 AN: 879710 Hom.: 0 AF XY: 0.00000458 AC XY: 2 AN XY: 437024

African (AFR) AF: 0.00 AC: 0 AN: 17788

American (AMR) AF: 0.00 AC: 0 AN: 13256

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13542

East Asian (EAS) AF: 0.00 AC: 0 AN: 29396

South Asian (SAS) AF: 0.00 AC: 0 AN: 43464

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24420

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2684

European-Non Finnish (NFE) AF: 0.00000574 AC: 4 AN: 697318

Other (OTH) AF: 0.00 AC: 0 AN: 37842

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs755031728; hg19: chr1-151733379;